Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1141 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0602403184 sf0602402185 6 2403184 1.74E-117 7.00E-24
vg0602416881 sf0602415882 6 2416881 6.88E-117 9.51E-24
vg0602358935 sf0602357936 6 2358935 2.81E-113 6.57E-24
vg0526848842 sf0526786200 5 26848842 1.16E-63 NA
vg0626748458 sf0626747461 6 26748458 2.26E-61 NA
vg0623774685 sf0623773688 6 23774685 1.10E-60 NA
vg0113993155 sf0113992129 1 13993155 1.23E-60 NA
vg1221504838 sf1221471385 12 21504838 NA 2.20E-09
vg0325722534 sf0325720552 3 25722534 NA 2.04E-08
vg0728442720 sf0728441728 7 28442720 NA 2.48E-08
vg0419360666 sf0419188704 4 19360666 NA 7.32E-08
vg1022381249 sf1022309723 10 22381249 NA 8.33E-08
vg1206967731 sf1206966621 12 6967731 NA 1.96E-07
vg0616470948 sf0616469950 6 16470948 NA 2.24E-07
vg0201592768 sf0201592768 2 1592768 NA 4.97E-07
vg0713786254 sf0713785261 7 13786254 NA 7.87E-07
vg0631155509 sf0631154511 6 31155509 NA 1.12E-06
vg1221533276 sf1221499823 12 21533276 NA 1.17E-06
vg0317064370 sf0317063184 3 17064370 NA 1.21E-06
vg0806359109 sf0806358114 8 6359109 NA 1.23E-06
vg1219816099 sf1219787569 12 19816099 NA 1.48E-06
vg1127077893 sf1126606280 11 27077893 NA 1.79E-06
vg1100433021 sf1100432024 11 433021 NA 1.85E-06
vg0219834070 sf0219828202 2 19834070 NA 2.22E-06
vg1219796116 sf1219767586 12 19796116 NA 2.32E-06
vg1127078255 sf1126606642 11 27078255 NA 2.67E-06
vg0622289516 sf0622288519 6 22289516 NA 3.30E-06
vg0602474331 sf0602473332 6 2474331 NA 3.36E-06
vg0613263498 sf0613262499 6 13263498 NA 3.86E-06
vg0806359100 sf0806358105 8 6359100 NA 4.57E-06